Related papers: Chimeric protein complexes in hybrid species gener…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Organisms that exploit different environments may experience a stochastic delay in adjusting their fitness when they switch habitats. We study two species whose fitness is determined by the species composition of the local environment, as…
Biological organisms often have elongated, flexible structures with some degree of chirality in their bodies or movements. In nature, these organisms frequently take advantage of self-encapsulation mechanisms that create folded…
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…
Biological membranes mainly consist of lipids and proteins. While the proteins have many functions as single molecules, the membrane as a whole displays physical properties that cannot be explained on the single molecule level. For example,…
Molecular biology features numerous complexes of proteins that coordinate in an interlocking fashion to fulfill different functions. Adaptive evolution explains some of this complexity, but needn't be the default when neutral explanations…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
If two species exhibit different nonlinear responses to a single shared resource, and if each species modifies the resource dynamics such that this favors its competitor, they may stably coexist. This coexistence mechanism, known as…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Microbiomes are complex systems comprised of many interacting species. Species can survive harsh or changing conditions by rapid adaptation, a process accelerated by the exchange of genetic material between different species through…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
It was hypothesized that the structures of biological transport networks are the result of either energy consumption or adaptation dynamics. Although approaches based on these hypotheses can produce optimal network and form loop structures,…
Many of the biological phenomena involve collective dynamics driven by self-propelled motion and nonequilibrium force (i.e., activity) that result in features unexpected from equilibrium physics. On the other hand, biological experiments…
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy…
An increasing number of proteins are being discovered with a remarkable and somewhat surprising feature, a knot in their native structures. How the polypeptide chain is able to knot itself during the folding process to form these highly…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly mitochondria, is increasingly being recognised as an…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…